Hi Katie,
On Tue, May 10, 2011 at 4:51 PM, Songer, Katherine B - DNR
<katherine.son...@wisconsin.gov> wrote:
> Hello R experts,
>
> I've used metaMDS to run NMDS on some fish abundance data, and am also
> working on correlating environmental data to the NMDS coordinates. I'm fairly
> new to metaMDS and NMDS in general, so I have what are probably some very
> basic questions. My fish abundance data consists of 66 sites for which up to
> 20 species of fish were identified and counted. I ran metaMDS on this data in
> 3 dimensions (after using a scree plot to check for stress levels in the
> different dimensions). I then used envfit to correlate a predictor dataset of
> environmental variables with the NMDS results, using the following code.
>
>>Fish<-as.data.frame(read.csv("Fish.csv",header=TRUE, sep = ","))
>>Fish.mds<-metaMDS(Fish,zerodist = "add",k=3,trymax=20)
>
>>Predictors<-as.data.frame(read.csv("Predictors.csv",header=TRUE, sep = ","))
>>Fish.fit <- envfit(Fish.mds$points, Predictors, k=3, 1000, na.rm = TRUE)
Have a look at the choices argument in envfit, etc. This is how you
specify which axes you want to plot.
ord <- metaMDS(varespec, k=3)
fit <- envfit(ord, varechem,
perm = 999, choices=c(1:3))
fit
plot(ord, choices=c(1,3))
plot(fit, choices=c(1,3))
>>Fish.fit
>
> The output of Fish.fit was as follows (table truncated):
>
> Dim1 Dim2 r2 Pr(>r)
> DrainArea -0.5923233 -0.8057004 0.7674 0.000999 ***
> Flow -0.5283236 -0.8490431 0.7847 0.000999 ***
> StrmWidth -0.6993457 -0.7147836 0.6759 0.000999 ***
> Gradient 0.4541225 0.8909392 0.2085 0.010989 *
>
> I'd like to better understand how to read this table. I understand that Dim1
> and Dim2 refer to the dimensions of the vectors produced by envfit, and r2 is
> the r-squared of those vectors. But how do I visualize these vectors in a 3-d
> plot? To which of the 3 NMDS dimensions are these vectors being correlated?
> Is there code to produce the x, y, and z coordinates of each of the sites in
> Fish.mds?
>
> Thanks very much.
> Katie
>
>
> [[alternative HTML version deleted]]
>
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>
--
Michael Denslow
I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.
-- AND --
Communications Manager
Southeast Regional Network of Expertise and Collections
sernec.org
36.214177, -81.681480 +/- 3103 meters
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